Gene loci information

Transcript annotation

  • This transcript has been annotated as Pre-mRNA-splicing factor 38B.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g10182 g10182.t10 TSS g10182.t10 8137442 8137442
chr_1 g10182 g10182.t10 isoform g10182.t10 8138263 8139870
chr_1 g10182 g10182.t10 exon g10182.t10.exon1 8138263 8138278
chr_1 g10182 g10182.t10 cds g10182.t10.CDS1 8138263 8138278
chr_1 g10182 g10182.t10 exon g10182.t10.exon2 8138363 8138476
chr_1 g10182 g10182.t10 cds g10182.t10.CDS2 8138363 8138476
chr_1 g10182 g10182.t10 exon g10182.t10.exon3 8138700 8138790
chr_1 g10182 g10182.t10 cds g10182.t10.CDS3 8138700 8138790
chr_1 g10182 g10182.t10 exon g10182.t10.exon4 8139024 8139066
chr_1 g10182 g10182.t10 cds g10182.t10.CDS4 8139024 8139066
chr_1 g10182 g10182.t10 exon g10182.t10.exon5 8139156 8139259
chr_1 g10182 g10182.t10 cds g10182.t10.CDS5 8139156 8139259
chr_1 g10182 g10182.t10 exon g10182.t10.exon6 8139327 8139870
chr_1 g10182 g10182.t10 cds g10182.t10.CDS6 8139327 8139870
chr_1 g10182 g10182.t10 TTS g10182.t10 8140068 8140068

Sequences

>g10182.t10 Gene=g10182 Length=912
ATGGCGGATGAACAAGAATATAGTGGAGGAAAAAAGAAAAATAATAGTTTACCTATCTAT
GGAAATCATGAAACGATGAATCTTAATAACTTAATTTTAACAAATATTCAATCAAGTGTT
TATTTCAAAGTGACATTATTTCAGCTGAAAACGTATCATGAAGTCATTGATGAAATCTAC
TATCAAGTAAAACATCTTGAGCCTTGGGAACTTAATTCCCGGAGCGTAAGGGGAGTGGGC
TCGGGTGGAATAGTTAGTAGTGCATTTTGTCTTTTATACAAACTATATACACTGAAATTG
ACACGAAAACAGCTAAATGGTTTAATAAAGCATACAGATTCGCCATATATCCGTGCTTTA
GGATTCATGTATATTCGCTACACTCAACCTCCTGCTGATTTATTTGGATGGTATGAGGAG
TTTCTTCAAGATGAAGAAGAGATTGATATTAAAGCTGGTGGAGGCCATATTTTGACAATA
GGTCAAATGTGTAGACAATTCCTTGTAAAGCTCGATTGGTTTAGTACACTCTTTCCACGA
ATTCCTGTTCCAATACAAAAAAGTATAGAACAGCGATTAAATGACTATGACAAACAAAAT
GGAATTGTAGCTCAACCAATTGTTTCCATCCCACAACAACCAGAACGACGTGAACGCTCT
TCAAAAGAGTATTACAGAAGTGAAAGGAGACGTTCTCGATCACCGATAGCGAAGCGTTCA
CGATCACCAACAGAAAGGCGTTATAGAGGTGACTTTGATGATGACGCAAGACATTCAAGA
CGATCACATAGCCGAGAGAAATATTCATCAAGTAAGTCTTCAAAGTATTATAGAGATCGT
TCAAGATCTCGTTCTAGAGAACGTAATGATCGAAGAAGATACGAAGAATCGAGAAGTTCA
CGTCGTTATTAA

>g10182.t10 Gene=g10182 Length=303
MADEQEYSGGKKKNNSLPIYGNHETMNLNNLILTNIQSSVYFKVTLFQLKTYHEVIDEIY
YQVKHLEPWELNSRSVRGVGSGGIVSSAFCLLYKLYTLKLTRKQLNGLIKHTDSPYIRAL
GFMYIRYTQPPADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPR
IPVPIQKSIEQRLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRS
RSPTERRYRGDFDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSS
RRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10182.t10 MobiDBLite mobidb-lite consensus disorder prediction 211 303 -
5 g10182.t10 MobiDBLite mobidb-lite consensus disorder prediction 215 231 -
4 g10182.t10 MobiDBLite mobidb-lite consensus disorder prediction 238 303 -
2 g10182.t10 PANTHER PTHR23142 UNCHARACTERIZED 7 302 9.6E-103
3 g10182.t10 PANTHER PTHR23142:SF2 PRE-MRNA-SPLICING FACTOR 38B 7 302 9.6E-103
1 g10182.t10 Pfam PF03371 PRP38 family 18 189 3.0E-52

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed